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Development of SNP Panels as a New Tool to Assess the Genetic Diversity, Population Structure, and Parentage Analysis of the Eastern Oyster (Crassostrea virginica)

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Abstract

Culture of the eastern oyster (Crassostrea virginica) is rapidly expanding. Combined with their continuing role as an environmental sentinel species and ecological model, this trend necessitates improved molecular tools for breeding and selection, as well as population assessment and genetic conservation. Here, we describe the development and validation of two panels of 58 single nucleotide polymorphism markers (SNPs) for the species. Population analyses revealed three distinct populations, based on FST values and STRUCTURE, among wild oysters sampled from Delaware Bay (1), northwest Florida (2), Alabama (2), Louisiana (2), and the Texas Gulf Coast (3), consistent with previous microsatellite and mtDNA analyses. In addition, utilizing the developed panels for parentage assignment in cultured oysters (Rutgers, New Jersey) resulted in a highly accurate identification of parent pairs (99.37%). The SNP markers could, furthermore, clearly discriminate between hatchery stocks and wild-sourced individuals. The developed SNP panels may serve as an important tool for more rapid and affordable genetic analyses in eastern oyster.

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Acknowledgements

This research was carried out with a part of a grant from The Gulf of Mexico Research Initiative through the Alabama Center for Ecological Resilience Consortium administered by the Dauphin Island Sea Lab. The authors are grateful to Perry R. Bass Marine Fisheries Research Station, Texas Parks and Wildlife, especially Joel D. Anderson for supplying Texas oyster DNA samples. Wilawan Thongda personally thanks the Royal Thai Government for their support of her study at Auburn University.

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Authors and Affiliations

  1. School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA

    Wilawan Thongda, Honggang Zhao, Dongdong Zhang, Lauren N. Jescovitch & Eric Peatman

  2. Institute of Marine and Coastal Sciences and The New Jersey Agricultural Experiment Station, Haskin Shellfish Research Laboratory, Rutgers University, Port Norris, NJ, 08349, USA

    Ming Liu & Ximing Guo

  3. Department of Marine Sciences, University of South Alabama, Mobile, AL, 36688, USA

    Meagan Schrandt & Sean P. Powers

  4. Center for Ecosystem Based Fisheries Management, Dauphin Island Sea Lab, Dauphin Island, AL, 36528, USA

    Meagan Schrandt & Sean P. Powers

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  1. Wilawan Thongda
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  2. Honggang Zhao
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  3. Dongdong Zhang
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  4. Lauren N. Jescovitch
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  5. Ming Liu
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  6. Ximing Guo
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  7. Meagan Schrandt
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  8. Sean P. Powers
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  9. Eric Peatman
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Correspondence to Eric Peatman.

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Thongda, W., Zhao, H., Zhang, D. et al. Development of SNP Panels as a New Tool to Assess the Genetic Diversity, Population Structure, and Parentage Analysis of the Eastern Oyster (Crassostrea virginica). Mar Biotechnol 20, 385–395 (2018). https://doi.org/10.1007/s10126-018-9803-y

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